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NEOS Interfaces to ECM

WWW Form & Sample Submissions
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XML-RPC

ECM

The NEOS Server offers the ECM solver to optimize enzyme profiles and corresponding metabolite profiles that realize a desired flux at minimum cost. The required data must be specified in a set of required files in CSV format. The Enzyme Cost Minimization case study on the NEOS Guide describes the problem in more detail. The ECM solver was developed by Meike Wortel and Michael Ferris.


Using the NEOS Server with ECM

The user must provide the required data files in the CSV format specified below and select a nonlinear programming solver.


Web Submission Form
stoich
Stoichiometry data (required): each row has format rateID,metaboliteID,value
keqs
Equilibrium constants: each row has format rateID,value. Reactions not supplied are irreversible.
kcats
Turnover numbers (required)
kms
Michaelis constants
metfixed
Fixed metabolite levels
rates
List of flux modes (required): each row has format efmnumber,rateID1,rateID2,... The efmnumber should be an integer.
boundse
Bounds on enzyme levels (optional)
boundsx
Bounds on metabolite levels (optional)
moietymet
Metabolites in moieties (optional)
moietyval
Total moiety concentrations (optional)
weights
Enzyme weights (optional): taken as value of 1 if not specified
activators
Optional: only provide if activator exists
inhibitors
Optional: only provide if inhibitor exists
alpha
alpha values (optional): advanced option for custom rate equations
A
A values (optional): advanced option for custom rate equations
Nonlinear Solver
Select an NLP solver
BARON
CONOPT
IpoptH
Knitro
LINDOGlobal
SNOPT
Additional Settings
Dry run: generate job XML instead of submitting it to NEOS
Short Priority: submit to higher priority queue with maximum CPU time of 5 minutes
E-Mail address:
Please do not click the 'Submit to NEOS' button more than once.